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The water lily clade represents the second earliest diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, whose dominant clade (the “core Nymphaeaceae”) comprises the genera Barclaya, Euryale, Nymphaea, and Victora. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. Among these unresolved questions are (i) the potential sister relationship of Euryale and Victoria to the subgenera Hydrocallis and Lotos of Nymphaea, which would render Nymphaea paraphyletic, (ii) the potential sister relationship of the type subgenus of Nymphaea to all other species of the genus, and (iii) the unclear relationships within the subgenera Brachyceras, Hydrocallis, and Nymphaea of Nymphaea. New molecular phylogenetic studies on the core Nymphaeaceae need to accommodate the idiosyncrasies of the non-coding plastome regions, as most of the DNA sequence variability and, by extension, phylogenetic information between the water lily genomes is located in the length-variable introns and intergenic spacers. For example, new studies must emphasize correct, motif-based DNA sequence alignments of intron and intergenic spacer regions before phylogenetic tree reconstruction. In this study, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomics analysis strategy in which the coding and non-coding partitions of the plastome are separated by region and undergo an automatic as well as a manual DNA sequence alignment. Our approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through automated algorithms. It produces significantly different phylogenetic tree reconstructions for several of the regions under study. The results of these reconstructions indicate that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the type subgenus is sister to all other subgenera of Nymphaea. Our results also clarify many relationships within the Nymphaea subgenera Brachyceras, Hydrocallis, and Nymphaea. Finally, we discuss whether the phylogenetic reconstructions received through our approach are in line with morphological evidence.

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuensecompared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice. &nbsp

High Andean forests harbor a remarkably high biodiversity and play a key role in providing vital ecosystem services for neighboring cities and settlements. However, they are among the most fragmented and threatened ecosystems in the neotropics. To preserve their unique biodiversity, a deeper understanding of the effects of anthropogenic perturbations on them is urgently needed. Here, we characterized the plant communities of high Andean forest remnants in the hinterland of Bogotá in 32 0.04 ha plots. We assessed the woody vegetation and sampled the understory and epiphytic cover. We gathered data on compositional and structural parameters and compiled a broad array of variables related to anthropogenic disturbance, ranging from local to landscape‐wide metrics. We also assessed phylogenetic diversity and functional diversity. We employed nonmetric multidimensional scaling (NMDS) to select meaningful variables in a first step of the analysis. Then, we performed partial redundancy analysis (pRDA) and generalized linear models (GLMs) in order to test how selected environmental and anthropogenic variables are affecting the composition, diversity, and aboveground biomass of these forests. Identified woody vegetation and understory layer communities were characterized by differences in elevation, temperature, and relative humidity, but were also related to different levels of human influence. We found that the increase of human‐related disturbance resulted in less phylogenetic diversity and in the phylogenetic clustering of the woody vegetation and in lower aboveground biomass (AGB) values. As to the understory, disturbance was associated with a higher diversity, jointly with a higher phylogenetic dispersion. The most relevant disturbance predictors identified here were as follows: edge effect, proximity of cattle, minimum fragment age, and median patch size. Interestingly, AGB was efficiently predicted by the proportion of late successional species. We therefore recommend the use of AGB and abundance of late successional species as indicators of human disturbance on high Andean forests., High Andean forests play a key role in providing ecosystem services for neighboring urban settlements. Here, we aimed to identify and understand the effects of anthropogenic perturbations on diversity, composition, and structure of plant communities, as well as aboveground biomass in high Andean forest remnants in the hinterland of Bogotá. We found that the increase of human‐related disturbance resulted in less phylogenetic diversity and in the phylogenetic clustering of the woody vegetation and in lower aboveground biomass (AGB) values. As to the understory, disturbance was associated with a higher diversity, jointly with a higher phylogenetic dispersion. Interestingly, AGB was efficiently predicted by the proportion of late successional species.

Scutellaria is one of the largest genera in the Lamiaceae with an estimated 400���500 species with a nearly worldwide distribution. Most species occur in the N hemisphere, with the Caucasus and the wider Irano-Turanian region housing a large number of taxa, many of them considered endemic. We present an overall phylogeny of the monophyletic genus Scutellaria based on rapidly evolving plastid regions (matK-trnK, rpl16, trnL-F). Three well-supported clades are evident, which render the currently accepted S. subg. Scutellaria paraphyletic to S. subg. Apeltanthus, which appears nested in ���clade A���, in which the African S. schweinfurthii is sister to all remaining taxa, followed by other lineages of S. subg. Scutellaria. Ancestral states of 12 morphological characters frequently used as diagnostic from subgenus to species level were reconstructed with BayesTraits. The S. orientalis group appears as a major radiation in the Caucasus area and the Irano-Turanian region that may comprise up to a quarter of the species in the genus. This radiation corresponds to a monophyletically defined S. sect. Lupulinaria, characterized by decussate inflorescences and specialized (e.g. cucullate) bracts. Our phylogenetic data present significant resolution at the species level within the S. orientalis group, indicating complex geographically centred patterns of speciation in adaptation to steppe and high mountain habitats, including multiple evolution of pinnate and tomentose leaves. The detailed infrageneric classification of Juzepczuk (1951, 1954) mostly does not reflect natural groups.